Iterativno traženje motiva i vreća fraza u genomu i proteomu

master's thesis

• Author: Anamarija Čavka
• Mentor: Pavle Goldstein (mentor)
• Committee member: Pavle Goldstein (predsjednik povjerenstva)
• Committee member: Damir Bakić (član povjerenstva)
• Committee member: Boris Guljaš (član povjerenstva)
• Committee member: Eduard Marušić-Paloka (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Mathematics); Zagreb
• Defense date and country: 2018-11-28, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Mathematics

Abstract

Cilj ovog diplomskog rada bio je testirati algoritam iterativnog pretraživanja te analizirati rezultate ovisno o parametrima. Također, važno je bilo usporediti te rezultate s rezultatima sličnog algoritma na analognom problemu. Za analizu smo odabrali genom i proteom krumpira te proteinsku familiju GDSL lipaza krumpira. Na tim nizovima genoma proveli smo postupak traženja specifičnog motiva proteinske familije GDSL lipaza krumpira kojeg smo prethodno preveli u alfabet genoma. Cilj je bio identificirati sve one nizove na genomu koji kodiraju proteinsku familiju GDSL lipaza. Analizirali smo naše rezultate te ih usporedili s rezultatima na proteomu. Zaključili smo kako je ponašanje na našem primjeru poprilično loše. Međutim, postoje indicije kako algoritam sam po sebi nije problem. Problem vjerojatno leži u nedostatku konzistentne anotacije na biološkim nizovima, različitim biološkim procesima zbog kojih naše aproksimacije unose prevelik kaos te u većoj varijabilnosti na genomu naspram proteoma.

Abstract (english)

This thesis is concerned with an iterative search algorithm and the analysis of its results with respect to various choices of parameters. Furthermore, it was important to compare these results with results of a similar algorithm on an analogous problem. For the analysis, we chose the potato genome and proteome and the GDSL lipase protein family. We applied the iterative search algorithm on genome sequences in order to find the specific motif of the GDSL lipase protein family which was translated to the alphabet of the genome earlier in the thesis. The goal was to identify all those genome sequences which code the potato’s GDSL lipase protein family. Finally, we analyzed our results in comparison to those obtained by proteome analysis. We concluded that the results were rather poor. However, there are indications that the algorithm itself is not as problematic as the results would imply. It is likely that the problem lies in the lack of consistent annotation of biological sequences, different biological processes due to which our approximations create far too much chaos, and in the greater variability of the genome when compared to proteom.

• Keywords: algoritam iterativnog pretraživanja; genom krumpira; proteom krumpira; GDSL lipaza; traženje specifičnog motiva
• Keywords (english): iterative search algorithm; potato genome; potato proteome; GDSL lipase; finding specific motifs
• Language: croatian
• URN:NBN: urn:nbn:hr:217:357042
• Study programme: Title: Mathematical Statistics; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra matematike (magistar/magistra matematike)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access
• Created on: 2019-03-27 13:28:59